Support blast and diamond blastp for ortholog identification (#643)

* add ignore zero anchor parameter for skip no matches in batch search

* ignore blank line in bed

* set label/chr size in layout file

* add genelabel rotation (customize x and y for rotation with angle 0)

* add customize x y for genelabelrotation 0; add --outputprefix for customized output

* Reverting some changes when I messed up the "Resolving Conflicts" step

* add blast diamond blastp

---------

Co-authored-by: Haibao Tang <tanghaibao@gmail.com>

jcvi/apps/align.py

@@ -31,6 +31,13 @@ def run_formatdb(infile=None, outfile=None, dbtype="nucl"):
     sh(cmd)
 
 
+@depends
+def run_diamond_makedb(infile=None, outfile=None):
+    cmd = "diamond makedb"
+    cmd += " --in {0} --db {1} -p 5".format(infile, infile)
+    sh(cmd)
+
+
 @depends
 def run_blat(
     infile=None,
@@ -586,5 +593,126 @@ def last(args, dbtype=None):
     return lastfile
 
 
+def blast_main(args, dbtype=None):
+    """
+    %prog database.fasta query.fasta
+
+    Run blastp/blastn by calling BLAST+ blastp/blastn depends on dbtype.
+    """
+    p = OptionParser(blast_main.__doc__)
+    p.add_option(
+        "--dbtype",
+        default="nucl",
+        choices=("nucl", "prot"),
+        help="Molecule type of subject database",
+    )
+    p.add_option("--path", help="Specify BLAST path for blastn or blastp")
+
+    p.set_cpus()
+    p.set_outdir()
+    p.set_params()
+
+    opts, args = p.parse_args(args)
+
+    if len(args) != 2:
+        sys.exit(not p.print_help())
+
+    subject, query = args
+    path = opts.path
+    cpus = opts.cpus
+    if not dbtype:
+        dbtype = opts.dbtype
+
+    getpath = lambda x: op.join(path, x) if path else x
+    cmd = "blastn" if dbtype == "nucl" else "blastp"
+    lastdb_bin = getpath("makeblastdb")
+    lastal_bin = getpath(cmd)
+    for bin in (lastdb_bin, lastal_bin):
+        if not which(bin):
+            logging.fatal("`%s` not found on PATH. Have you installed BLAST?", bin)
+            sys.exit(1)
+
+    db_suffix = '.nin' if dbtype == "nucl" else ".pin"
+
+    run_formatdb(
+        infile=subject,
+        outfile=subject + db_suffix,
+        dbtype=dbtype)
+
+    blastfile = get_outfile(subject, query, suffix="last", outdir=opts.outdir)
+    # Make several attempts to run LASTAL
+    try:
+        sh(
+            cmd + f" -num_threads {cpus} -query {query} -db {subject} -out {blastfile}" +
+            " -outfmt 6 -max_target_seqs 1000 -evalue 1e-5",
+            check=False,
+            redirect_error=STDOUT,
+        )
+    except CalledProcessError as e:  # multi-threading disabled
+        message = f"{cmd} failed with message:"
+        message += "\n{0}".format(e.output.decode())
+        logging.error(message)
+        logging.fatal("Failed to run `blast`. Aborted.")
+        cleanup(blastfile)
+        sys.exit(1)
+    return blastfile
+
+
+def diamond_blastp_main(args, dbtype="prot"):
+    """
+    %prog database.fasta query.fasta
+
+    Run diamond blastp for protein alignment.
+    """
+    p = OptionParser(diamond_blastp_main.__doc__)
+
+    p.add_option("--path", help="Specify diamond path for diamond blastp")
+
+    p.set_cpus()
+    p.set_outdir()
+    p.set_params()
+
+    opts, args = p.parse_args(args)
+
+    if len(args) != 2:
+        sys.exit(not p.print_help())
+
+    subject, query = args
+    path = opts.path
+    cpus = opts.cpus
+    if not dbtype:
+        dbtype = opts.dbtype
+
+    getpath = lambda x: op.join(path, x) if path else x
+    cmd = "diamond blastp"
+    diamond_bin = getpath("diamond")
+    for bin in (diamond_bin,):
+        if not which(bin):
+            logging.fatal("`%s` not found on PATH. Have you installed Diamond?", bin)
+            sys.exit(1)
+
+    run_diamond_makedb(
+        infile=subject,
+        outfile=subject + '.dmnd',)
+
+    blastfile = get_outfile(subject, query, suffix="last", outdir=opts.outdir)
+    # Make several attempts to run LASTAL
+    try:
+        sh(
+            cmd + f" --threads {cpus} --query {query} --db {subject} --out {blastfile}" +
+            " --ultra-sensitive --max-target-seqs 1000 --evalue 1e-5 --outfmt 6",
+            check=False,
+            redirect_error=STDOUT,
+        )
+    except CalledProcessError as e:  # multi-threading disabled
+        message = f"{cmd} failed with message:"
+        message += "\n{0}".format(e.output.decode())
+        logging.error(message)
+        logging.fatal("Failed to run `diamond blastp`. Aborted.")
+        cleanup(blastfile)
+        sys.exit(1)
+    return blastfile
+
+
 if __name__ == "__main__":
     main()

jcvi/compara/catalog.py

@@ -609,6 +609,7 @@ def ortholog(args):
     match (RBH).
     """
     from jcvi.apps.align import last as last_main
+    from jcvi.apps.align import diamond_blastp_main, blast_main
     from jcvi.compara.blastfilter import main as blastfilter_main
     from jcvi.compara.quota import main as quota_main
     from jcvi.compara.synteny import scan, mcscan, liftover
@@ -621,6 +622,7 @@ def ortholog(args):
         choices=("nucl", "prot"),
         help="Molecule type of subject database",
     )
+
     p.add_option(
         "--full",
         default=False,
@@ -673,6 +675,13 @@ def ortholog(args):
         help="Ignore this pair of ortholog identification instead of throwing an error when performing many pairs of cataloging."
     )
 
+    p.add_option(
+        "--align_soft",
+        default="last",
+        choices=("last", "blast", "diamond_blastp"),
+        help="Sequence alignment software. Default <last> for both <nucl> and <prot>. Users could also use <blast> for both <nucl> and <prot>, or <diamond_blastp> for <prot>.",
+    )
+
     opts, args = p.parse_args(args)
 
     if len(args) != 2:
@@ -690,14 +699,24 @@ def ortholog(args):
     dist = "--dist={0}".format(opts.dist)
     minsize_flag = "--min_size={}".format(opts.n)
     cpus_flag = "--cpus={}".format(opts.cpus)
+    align_soft = opts.align_soft
 
     aprefix = op.basename(a)
     bprefix = op.basename(b)
     pprefix = ".".join((aprefix, bprefix))
     qprefix = ".".join((bprefix, aprefix))
     last = pprefix + ".last"
     if need_update((afasta, bfasta), last, warn=True):
-        last_main([bfasta, afasta, cpus_flag], dbtype)
+        if align_soft == "blast":
+            blast_main(
+                [bfasta, afasta, cpus_flag], dbtype
+            )
+        elif dbtype == "prot" and align_soft == "diamond_blastp":
+            diamond_blastp_main(
+                [bfasta, afasta, cpus_flag], dbtype
+            )
+        else:
+            last_main([bfasta, afasta, cpus_flag], dbtype)
 
     self_remove = opts.self_remove
     if a == b: